@article{20924,
  abstract     = {Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during cellular differentiation and reprogramming. Here, we present selected engagement on nucleosome sequencing (SeEN-seq), a protocol designed to systematically identify potential TF-binding sites on the nucleosome. We describe steps for nucleosome library assembly, SeEN-seq assay, and cryoelectron microscopy (cryo-EM) sample preparation. This protocol facilitates the preparation of homogeneous pioneer TF-nucleosome complexes for cryo-EM structure determination using single-particle analysis.
For complete details on the use and execution of this protocol, please refer to Michael et al.1},
  author       = {Kobayashi, Wataru and Michael, Alicia and Ruangroengkulrith, Siwat and Kümmecke, Maximilian and Tachibana, Kikuë},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {1},
  publisher    = {Elsevier},
  title        = {{Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination}},
  doi          = {10.1016/j.xpro.2025.104295},
  volume       = {7},
  year         = {2026},
}

@article{22720,
  abstract     = {Circadian clocks underlie daily rhythms in physiology by coordinating temporal patterns of gene expression and protein function throughout the body. At the core of this system in mammals is CLOCK/BMAL1, a ubiquitously expressed heterodimeric transcription factor complex that orchestrates tissue-specific circadian gene expression. The basis for this specificity remains unclear, but tissue-specific interactions at chromatin could provide one. Here we used chromatin immunoprecipitation coupled to mass spectrometry to map CLOCK/BMAL1-associated protein complexes on chromatin in mouse liver, kidney and lung. We detected 1,510 associated proteins, most of which were tissue-specific and not explained by protein abundance. Among these, we identified the homeodomain transcription factors PROX1, HNF1B and HOXA5 as tissue-enriched interactors that bind BMAL1, co-occupy most BMAL1 genomic sites and establish organ-restricted circadian transcription. Our findings demonstrate that tissue-specific transcription factors confer cellular identity on the core clock, thereby contributing to organ-specific patterns of rhythmic gene expression.},
  author       = {Aygenli, Fatih and Huschet, Lukas A. and Popp, Tanja and Ribeiro, Andrea and Barkhatova, Darina and Jouffe, Céline and Trozzo, Ricardo and Menet, Jerome S. and Rad, Roland and Dyar, Kenneth A. and Lech, Maciej and Straub, Tobias and Michael, Alicia and Robles, Maria S.},
  issn         = {1476-4679},
  journal      = {Nature Cell Biology},
  publisher    = {Springer Nature},
  title        = {{CLOCK/BMAL1 interactome uncovers homeodomain factors as tissue regulators}},
  doi          = {10.1038/s41556-026-02041-4},
  year         = {2026},
}